PLINK is a free,
open-source whole genome association analysis toolset, designed to perform
a range of basic, large-scale analyses in a computationally efficient
manner.
The focus of PLINK
is purely on analysis of genotype/phenotype data, so
there is no support for steps prior to this (e.g. study design
and planning, generating genotype or CNV calls from raw data).
Through integration with gPLINK and
Haploview,
there is some support for the subsequent visualization, annotation
and storage of results.
PLINK (one syllable) is
being developed by Shaun Purcell whilst at the
Center for Human Genetic Research (CHGR),
Massachusetts General Hospital (MGH), and the Broad Institute of Harvard & MIT,
with the support of others.
New in 1.07: meta-analysis, result annotation
and analysis of dosage data.